5V4D

Crystal Structure of the Protein of Unknown Function of the Conserved Rid Protein Family YyfA from Yersinia pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.153

Literature

Macromolecules
Sequence Display for 5V4D

Classification: Structural genomics unknown function

Total Structure Weight: 83194.10

Macromolecule Entities
Molecule Chains Length Organism Details
Putative translational inhibitor protein A, B, C..., D, E, FA, B, C, D, E, F 128 Yersinia pestis Gene Name(s): tdcF3 y3551 YP_2944 YPO0627
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A, C, E GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A, B, C, D, E, F ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, E, F CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.180
  • R-Value Work: 0.153
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 67.93 α = 90.00
b = 80.92 β = 90.00
c = 141.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2017-03-09
  • Released Date: 2017-04-05
  • Deposition author(s): Kim, Y., Chhor, G., Endres, M., Krishnan, A., Babnigg, G., Schneewind, O., Anderson, W.F., Joachimiak, A., Chicago Center for Functional Genomics, Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

No revisions since initial release